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- PDB-4pgz: Structural basis of KIT activation by oncogenic mutations in the ... -

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Basic information

Entry
Database: PDB / ID: 4pgz
TitleStructural basis of KIT activation by oncogenic mutations in the extracellular region reveals a zipper-like mechanism for ligand-dependent or oncogenic receptor tyrosine kinase activation
ComponentsMast/stem cell growth factor receptor Kit
KeywordsTRANSFERASE / Receptor Tyrosine Kinase / KIT receptor / IgSF / cancer / surface receptor
Function / homology
Function and homology information


Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants / Nilotinib-resistant KIT mutants / Regorafenib-resistant KIT mutants / Signaling by kinase domain mutants of KIT / Sunitinib-resistant KIT mutants / Signaling by juxtamembrane domain KIT mutants / Sorafenib-resistant KIT mutants ...Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants / Nilotinib-resistant KIT mutants / Regorafenib-resistant KIT mutants / Signaling by kinase domain mutants of KIT / Sunitinib-resistant KIT mutants / Signaling by juxtamembrane domain KIT mutants / Sorafenib-resistant KIT mutants / Signaling by extracellular domain mutants of KIT / hematopoietic stem cell migration / melanocyte adhesion / positive regulation of pyloric antrum smooth muscle contraction / positive regulation of colon smooth muscle contraction / positive regulation of vascular associated smooth muscle cell differentiation / melanocyte migration / Kit signaling pathway / regulation of bile acid metabolic process / positive regulation of dendritic cell cytokine production / positive regulation of small intestine smooth muscle contraction / mast cell chemotaxis / positive regulation of mast cell proliferation / mast cell differentiation / Fc receptor signaling pathway / glycosphingolipid metabolic process / mast cell proliferation / positive regulation of long-term neuronal synaptic plasticity / positive regulation of pseudopodium assembly / detection of mechanical stimulus involved in sensory perception of sound / positive regulation of mast cell cytokine production / lymphoid progenitor cell differentiation / melanocyte differentiation / immature B cell differentiation / germ cell migration / erythropoietin-mediated signaling pathway / myeloid progenitor cell differentiation / digestive tract development / negative regulation of programmed cell death / embryonic hemopoiesis / lamellipodium assembly / tongue development / positive regulation of tyrosine phosphorylation of STAT protein / Regulation of KIT signaling / megakaryocyte development / mast cell degranulation / stem cell population maintenance / pigmentation / positive regulation of Notch signaling pathway / growth factor binding / cytokine binding / negative regulation of reproductive process / negative regulation of developmental process / spermatid development / hemopoiesis / stem cell factor receptor activity / T cell differentiation / somatic stem cell population maintenance / ectopic germ cell programmed cell death / hematopoietic progenitor cell differentiation / response to cadmium ion / ovarian follicle development / positive regulation of DNA-binding transcription factor activity / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / SH2 domain binding / B cell differentiation / acrosomal vesicle / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / epithelial cell proliferation / erythrocyte differentiation / cell chemotaxis / positive regulation of receptor signaling pathway via JAK-STAT / stem cell differentiation / Signaling by SCF-KIT / receptor protein-tyrosine kinase / cytokine-mediated signaling pathway / visual learning / cytoplasmic side of plasma membrane / fibrillar center / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / cell-cell junction / PIP3 activates AKT signaling / regulation of cell shape / regulation of cell population proliferation / actin cytoskeleton organization / protein autophosphorylation / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / protein tyrosine kinase activity / spermatogenesis / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / intracellular signal transduction / positive regulation of cell migration
Similarity search - Function
Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Mast/stem cell growth factor receptor Kit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsReshetnyak, A.V. / Boggon, T.J. / Lax, I. / Schlessinger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Kolltan United States
CitationJournal: Mol.Cell / Year: 2015
Title: The strength and cooperativity of KIT ectodomain contacts determine normal ligand-dependent stimulation or oncogenic activation in cancer.
Authors: Reshetnyak, A.V. / Opatowsky, Y. / Boggon, T.J. / Folta-Stogniew, E. / Tome, F. / Lax, I. / Schlessinger, J.
History
DepositionMay 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / citation / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Mast/stem cell growth factor receptor Kit
A: Mast/stem cell growth factor receptor Kit
B: Mast/stem cell growth factor receptor Kit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,05111
Polymers70,0933
Non-polymers9588
Water1,47782
1
C: Mast/stem cell growth factor receptor Kit
hetero molecules

C: Mast/stem cell growth factor receptor Kit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4078
Polymers46,7282
Non-polymers6786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1900 Å2
ΔGint-30 kcal/mol
Surface area20360 Å2
MethodPISA
2
A: Mast/stem cell growth factor receptor Kit
B: Mast/stem cell growth factor receptor Kit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3487
Polymers46,7282
Non-polymers6195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-27 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.592, 63.548, 81.547
Angle α, β, γ (deg.)90.00, 117.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mast/stem cell growth factor receptor Kit / SCFR / Piebald trait protein / PBT / Proto-oncogene c-Kit / Tyrosine-protein kinase Kit / p145 c- ...SCFR / Piebald trait protein / PBT / Proto-oncogene c-Kit / Tyrosine-protein kinase Kit / p145 c-kit / v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog


Mass: 23364.225 Da / Num. of mol.: 3 / Fragment: UNP residues 308-514
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIT, SCFR / Cell line (production host): sf9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P10721, receptor protein-tyrosine kinase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 10%-18% [w/v] PEG 3350, 20 mM cobalt chloride

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2011
RadiationMonochromator: Si-111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 29387 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.108 / Χ2: 0.986 / Net I/av σ(I): 15.53 / Net I/σ(I): 8.3 / Num. measured all: 178278
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.495.30.82428670.80798.7
2.49-2.596.10.6529280.876100
2.59-2.76.10.44229210.926100
2.7-2.856.20.31629421.02899.9
2.85-3.026.10.21329391.035100
3.02-3.266.30.15129121.029100
3.26-3.586.20.11929261.062100
3.58-4.16.20.10129481.014100
4.1-5.176.20.08629701.049100
5.17-5060.0830340.993100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 2.4→42.39 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2617 1477 5.05 %
Rwork0.2318 --
obs0.2334 29249 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 47 82 4531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024564
X-RAY DIFFRACTIONf_angle_d0.6576214
X-RAY DIFFRACTIONf_dihedral_angle_d9.4841619
X-RAY DIFFRACTIONf_chiral_restr0.026693
X-RAY DIFFRACTIONf_plane_restr0.003805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.37581330.31782461X-RAY DIFFRACTION99
2.4775-2.5660.34941370.31362502X-RAY DIFFRACTION100
2.566-2.66870.3411210.30332529X-RAY DIFFRACTION100
2.6687-2.79020.35571290.29462538X-RAY DIFFRACTION100
2.7902-2.93720.30091160.28692504X-RAY DIFFRACTION100
2.9372-3.12120.31621390.28252532X-RAY DIFFRACTION100
3.1212-3.36210.32151660.25642483X-RAY DIFFRACTION100
3.3621-3.70030.2811340.23232530X-RAY DIFFRACTION100
3.7003-4.23530.25211370.2152521X-RAY DIFFRACTION100
4.2353-5.33430.18541580.18072530X-RAY DIFFRACTION100
5.3343-42.39680.24131070.21492642X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.20650.0931-1.94213.1221-2.11872.5613-0.7365-0.0161-0.69520.3446-0.1238-0.35590.46531.91770.47630.53380.03760.01030.7303-0.1060.3958-5-25.244377.6251
21.25270.9887-0.75486.7542-2.53365.62170.09790.38050.4011-1.2832-0.17090.37591.06760.1383-0.02730.5983-0.0751-0.13910.6858-0.05930.36-12.1605-17.531854.1833
33.6901-1.46592.08167.9775-7.00378.2132-0.2987-0.3108-0.2460.3450.08990.3067-0.32830.0839-0.24390.2975-0.0280.02410.5046-0.06990.3487-14.308-22.111972.8168
45.0918-1.32170.04573.0826-2.93523.1730.2764-0.52660.69980.1970.30132.5521-1.2954-0.2984-0.55120.71550.00230.00610.9374-0.03661.1231-21.1586-10.112566.6646
55.1902-3.22313.4014.751-4.20863.87180.2712-0.1342-0.82110.5260.62671.5314-0.11-0.2806-0.83140.4196-0.1415-0.02380.56270.09790.5673-17.848-31.303773.7002
62.0767-0.82010.9094.7716-4.55354.8525-0.2502-0.045-0.00770.0231.12910.9409-0.4167-1.2176-0.51320.5161-0.0631-0.0850.5682-0.0030.463-18.3949-17.80261.3502
72.8808-0.55280.66126.9841-4.72766.0741-0.12140.1682-0.09090.5234-0.18370.0655-1.48430.93730.27010.4219-0.0978-0.03550.5499-0.08170.307-10.5952-15.229468.5812
82.026-1.52390.3737.0087-3.9992.6872-0.1335-0.5791.33490.2191-1.5394-0.689-2.0704-0.72880.62961.2639-0.0629-0.57560.6097-0.14721.0605-14.35516.102242.309
90.6242-1.81590.9967.9483-4.72682.8885-1.03070.63782.47361.10150.3043-1.676-1.25810.97481.40560.6623-0.5165-0.2280.96590.46511.373-6.96113.504840.6324
107.0616-1.52023.70463.194-3.61294.9053-0.9982-1.4832.66691.6254-0.0639-1.0269-3.5427-0.61010.3491.0673-0.0207-0.28460.7421-0.42271.1923-12.95063.61248.746
111.28560.9801-2.53242.759-2.64625.2848-1.24540.77331.464-1.1240.6088-1.9662-1.35432.01851.11921.016-0.4785-0.12370.70380.34740.9241-11.51841.652435.0413
124.3382.0776-2.46343.95120.38946.60340.1996-0.00480.34610.05320.0367-0.1510.00870.1568-0.26760.4106-0.0283-0.02870.5073-0.05440.350140.3877-5.556-8.7719
137.43022.6363-1.70587.49341.41246.2099-0.58870.6580.2202-0.17340.14551.56130.3359-1.02340.30460.4036-0.0796-0.04820.53350.00590.629916.2131-6.419921.1329
147.12312.0378-0.41838.79313.80879.0643-0.19110.16620.13990.6625-0.4081.80690.6157-0.94650.30680.5049-0.09120.10920.4530.00690.675815.6702-7.164726.1288
155.43480.25853.92913.28770.25886.46750.6777-0.3477-0.9995-0.1376-0.13010.26210.716-0.6093-0.5910.5616-0.03-0.18750.5753-0.01090.7347.0298-1.614154.5439
165.76941.66681.44928.02782.32689.3527-0.05110.16111.3395-0.5483-0.25161.8065-1.0994-0.97540.05170.60550.1495-0.0310.43550.0050.984619.18978.94127.2349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 309 through 317 )
2X-RAY DIFFRACTION2chain 'C' and (resid 318 through 330 )
3X-RAY DIFFRACTION3chain 'C' and (resid 331 through 349 )
4X-RAY DIFFRACTION4chain 'C' and (resid 350 through 358 )
5X-RAY DIFFRACTION5chain 'C' and (resid 359 through 371 )
6X-RAY DIFFRACTION6chain 'C' and (resid 372 through 387 )
7X-RAY DIFFRACTION7chain 'C' and (resid 388 through 410 )
8X-RAY DIFFRACTION8chain 'C' and (resid 411 through 432 )
9X-RAY DIFFRACTION9chain 'C' and (resid 433 through 464 )
10X-RAY DIFFRACTION10chain 'C' and (resid 465 through 476 )
11X-RAY DIFFRACTION11chain 'C' and (resid 477 through 506 )
12X-RAY DIFFRACTION12chain 'A' and (resid 308 through 410 )
13X-RAY DIFFRACTION13chain 'A' and (resid 411 through 442 )
14X-RAY DIFFRACTION14chain 'A' and (resid 443 through 506 )
15X-RAY DIFFRACTION15chain 'B' and (resid 309 through 410 )
16X-RAY DIFFRACTION16chain 'B' and (resid 411 through 505 )

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